[gmx-users] MDRUN crash

Mark Abraham mark.j.abraham at gmail.com
Fri Jun 17 08:46:43 CEST 2016


Hi,

Please don't start new work with old out-of-maintenance software, or at
least use the most recent bug fix from that release branch. You should also
do an equilibration with a normal acetone first, so that you know whether
it's your equilibration or your shell model that is the problem.

Mark

On Fri, Jun 17, 2016 at 8:44 AM Luca Banetta <luca.banetta at gmail.com> wrote:

> thank you for the advice justin! i have made some research and i use PME
> for electrostatics that i noticed it's pretty common. Unfortunately the
> mdrun this fatal error appeared:
> Program mdrun, VERSION 4.5.4
> Source code file: pme.c, line: 538
>
> Fatal error:
> 1629 particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
>
> For out simulation we created a topology for the acetone molecule using
> opls-AA force field introudicing a shell particle inside the topology.
> At the moment the simulation is based on a single acetone molecule inside a
> "sea" of water.
> [ moleculetype ]
> ; Name            nrexcl
> acetone               3
>
> [ atoms ]
> ;   nr       type          resnr   residue      atom      cgnr   charge
> mass  typeB    chargeB    massB
>          1  opls_280         1       LIG         C         1      0.47
> 12.011
>          2  opls_135         1       LIG         C         2     -0.18
> 12.011
>          3  opls_135         1       LIG         C         3     -0.18
> 12.011
>          4  opls_281         1       LIG         O         4      0.47
> 15.5994
>          5  opls_282         1       LIG         H         5      0.06
> 1.008
>          6  opls_282         1       LIG         H         6      0.06
> 1.008
>          7  opls_282         1       LIG         H         7      0.06
> 1.008
>          8  opls_282         1       LIG         H         8      0.06
> 1.008
>          9  opls_282         1       LIG         H         9      0.06
> 1.008
>         10  opls_282        1       LIG         H        10      0.06
> 1.008
>         11     VS              1       LIG         VS       11
> -0.47     0.000
>         12     SP              1       LIG         SP       12
> -0.47     0.000
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     1     3     1
>     1     4     1
>     4     11    6
>     11    12    6
>     2     5     1
>     2     6     1
>     2     7     1
>     3     8     1
>     3     9     1
>     3    10     1
>
> [ pairs ]
> ;  ai    aj funct            c0            c1            c2            c3
>     2     8     1
>     2     9     1
>     2    10     1
>     3     5     1
>     3     6     1
>     3     7     1
>     4     5     1
>     4     6     1
>     4     7     1
>     4     8     1
>     4     9     1
>     4    10     1
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1
> c2            c3
>     2     1     3     1
>     2     1     4     1
>     3     1     4     1
>     1     2     5     1
>     1     2     6     1
>     1     2     7     1
>     5     2     6     1
>     5     2     7     1
>     6     2     7     1
>     1     3     8     1
>     1     3     9     1
>     1     3    10     1
>     8     3     9     1
>     8     3    10     1
>     9     3    10     1
>
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1
> c2            c3            c4            c5
>     3     1     2     5     3
>     3     1     2     6     3
>     3     1     2     7     3
>     4     1     2     5     3
>     4     1     2     6     3
>     4     1     2     7     3
>     2     1     3     8     3
>     2     1     3     9     3
>     2     1     3    10     3
>     4     1     3     8     3
>     4     1     3     9     3
>     4     1     3    10     3
>
> [ virtual_sites2 ]
> ; site  ai  aj  funct   a
>     11   1   4    1     1.05
>
> VS and SP have been introduced in the "ffnonbonded" and "ffbonded" sections
> in the library oplsaa.ff
>
> 2016-06-16 15:05 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 6/16/16 6:10 AM, Luca Banetta wrote:
> >
> >> Dear gmx users,
> >> I am meeting a lot of problems launching a simulation with shell
> >> particles.
> >> The mdp file is
> >> ; VARIOUS PREPROCESSING OPTIONS
> >> title                    = Yo
> >> cpp                      = /usr/bin/cpp
> >> include                  =
> >> define                   =
> >>
> >> ; RUN CONTROL PARAMETERS
> >> integrator               = md
> >> ; Start time and timestep in ps
> >> tinit                    = 0
> >> dt                       = 0.001
> >> nsteps                   = 1000000
> >> ; For exact run continuation or redoing part of a run
> >> init_step                = 0
> >> ; mode for center of mass motion removal
> >> comm-mode                = Linear
> >> ; number of steps for center of mass motion removal
> >> nstcomm                  = 1
> >> ; group(s) for center of mass motion removal
> >> comm-grps                =
> >>
> >> ; LANGEVIN DYNAMICS OPTIONS
> >> ; Temperature, friction coefficient (amu/ps) and random seed
> >> bd-temp                  = 300
> >> bd-fric                  = 0
> >> ld-seed                  = 1993
> >>
> >> ; ENERGY MINIMIZATION OPTIONS
> >> ; Force tolerance and initial step-size
> >> emtol                    = 100
> >> emstep                   = 0.01
> >> ; Max number of iterations in relax_shells
> >> niter                    = 20
> >> ; Step size (1/ps^2) for minimization of flexible constraints
> >> fcstep                   = 0
> >> ; Frequency of steepest descents steps when doing CG
> >> nstcgsteep               = 1000
> >> nbfgscorr                = 10
> >>
> >> ; OUTPUT CONTROL OPTIONS
> >> ; Output frequency for coords (x), velocities (v) and forces (f)
> >> nstxout                  =
> >> nstvout                  =
> >> nstfout                  =
> >> ; Checkpointing helps you continue after crashes
> >> nstcheckpoint            = 1000
> >> ; Output frequency for energies to log file and energy file
> >> nstlog                   = 50
> >> nstenergy                = 50
> >> ; Output frequency and precision for xtc file
> >> nstxtcout                = 50
> >> xtc-precision            = 1000
> >> ; This selects the subset of atoms for the xtc file. You can
> >> ; select multiple groups. By default all atoms will be written.
> >> xtc-grps                 =
> >> ; Selection of energy groups
> >> energygrps               =
> >>
> >> ; NEIGHBORSEARCHING PARAMETERS
> >> ; nblist update frequency
> >> nstlist                  = 5
> >> ; ns algorithm (simple or grid)
> >> ns_type                  = grid
> >> ; Periodic boundary conditions: xyz (default), no (vacuum)
> >> ; or full (infinite systems only)
> >> pbc                      = xyz
> >> ; nblist cut-off
> >> rlist                    = 0.9
> >> domain-decomposition     = no
> >>
> >> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> ; Method for doing electrostatics
> >> coulombtype              = Cut-off
> >> rcoulomb-switch          = 0
> >> rcoulomb                 = 0.9
> >> ; Dielectric constant (DC) for cut-off or DC of reaction field
> >> epsilon-r                = 1
> >> ; Method for doing Van der Waals
> >> vdw-type                 = Cut-off
> >> ; cut-off lengths
> >> rvdw-switch              = 0
> >> rvdw                     = 0.9
> >> ; Apply long range dispersion corrections for Energy and Pressure
> >> DispCorr                 = EnerPres
> >> ; Extension of the potential lookup tables beyond the cut-off
> >> table-extension          = 1
> >> ; Spacing for the PME/PPPM FFT grid
> >> fourierspacing           = 0.12
> >> ; FFT grid size, when a value is 0 fourierspacing will be used
> >> fourier_nx               = 0
> >> fourier_ny               = 0
> >> fourier_nz               = 0
> >> ; EWALD/PME/PPPM parameters
> >> pme_order                = 4
> >> ewald_rtol               = 1e-05
> >> ewald_geometry           = 3d
> >> epsilon_surface          = 0
> >> optimize_fft             = no
> >>
> >> ; GENERALIZED BORN ELECTROSTATICS
> >> ; Algorithm for calculating Born radii
> >> gb_algorithm             = Still
> >> ; Frequency of calculating the Born radii inside rlist
> >> nstgbradii               = 1
> >> ; Cutoff for Born radii calculation; the contribution from atoms
> >> ; between rlist and rgbradii is updated every nstlist steps
> >> rgbradii                 = 2
> >> ; Salt concentration in M for Generalized Born models
> >> gb_saltconc              = 0
> >>
> >> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> >> implicit_solvent         = No
> >>
> >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> >> ; Temperature coupling
> >> Tcoupl                   = berendsen
> >> ; Groups to couple separately
> >> tc-grps                  = System
> >> ; Time constant (ps) and reference temperature (K)
> >> tau_t                    = 0.1
> >> ref_t                    = 300
> >> ; Pressure coupling
> >> Pcoupl                   = berendsen
> >> Pcoupltype               = isotropic
> >> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >> tau_p                    = 1.0
> >> compressibility          = 4.5e-5
> >> ref_p                    = 1.0
> >> ; Random seed for Andersen thermostat
> >> andersen_seed            = 815131
> >>
> >> ; SIMULATED ANNEALING
> >> ; Type of annealing for each temperature group (no/single/periodic)
> >> annealing                = no
> >> ; Number of time points to use for specifying annealing in each group
> >> annealing_npoints        =
> >> ; List of times at the annealing points for each group
> >> annealing_time           =
> >> ; Temp. at each annealing point, for each group.
> >> annealing_temp           =
> >>
> >> ; GENERATE VELOCITIES FOR STARTUP RUN
> >> gen_vel                  = yes
> >> gen_temp                 = 300
> >> gen_seed                 = 1993
> >>
> >> ; OPTIONS FOR BONDS
> >> constraints              = all-bonds
> >> ; Type of constraint algorithm
> >> constraint-algorithm     = Lincs
> >> ; Do not constrain the start configuration
> >> unconstrained-start      = no
> >> ; Use successive overrelaxation to reduce the number of shake iterations
> >> Shake-SOR                = no
> >> ; Relative tolerance of shake
> >> shake-tol                = 1e-04
> >> ; Highest order in the expansion of the constraint coupling matrix
> >> lincs-order              = 4
> >> ; Number of iterations in the final step of LINCS. 1 is fine for
> >> ; normal simulations, but use 2 to conserve energy in NVE runs.
> >> ; For energy minimization with constraints it should be 4 to 8.
> >> lincs-iter               = 1
> >> ; Lincs will write a warning to the stderr if in one step a bond
> >> ; rotates over more degrees than
> >> lincs-warnangle          = 30
> >> ; Convert harmonic bonds to morse potentials
> >> morse                    = no
> >>
> >> ; ENERGY GROUP EXCLUSIONS
> >> ; Pairs of energy groups for which all non-bonded interactions are
> >> excluded
> >> energygrp_excl           =
> >>
> >> ; NMR refinement stuff
> >> ; Distance restraints type: No, Simple or Ensemble
> >> disre                    = No
> >> ; Force weighting of pairs in one distance restraint: Conservative or
> >> Equal
> >> disre-weighting          = Conservative
> >> ; Use sqrt of the time averaged times the instantaneous violation
> >> disre-mixed              = no
> >> disre-fc                 = 1000
> >> disre-tau                = 0
> >> ; Output frequency for pair distances to energy file
> >> nstdisreout              = 100
> >> ; Orientation restraints: No or Yes
> >> orire                    = no
> >> ; Orientation restraints force constant and tau for time averaging
> >> orire-fc                 = 0
> >> orire-tau                = 0
> >> orire-fitgrp             =
> >> ; Output frequency for trace(SD) to energy file
> >> nstorireout              = 100
> >> ; Dihedral angle restraints: No, Simple or Ensemble
> >> dihre                    = No
> >> dihre-fc                 = 1000
> >> dihre-tau                = 0
> >> ; Output frequency for dihedral values to energy file
> >> nstdihreout              = 100
> >>
> >> ; Free energy control stuff
> >> free-energy              = no
> >> init-lambda              = 0
> >> delta-lambda             = 0
> >> sc-alpha                 = 0
> >> sc-sigma                 = 0.3
> >>
> >> ; Non-equilibrium MD stuff
> >> acc-grps                 =
> >> accelerate               =
> >> freezegrps               =
> >> freezedim                =
> >> cos-acceleration         = 0
> >>
> >> ; Electric fields
> >> ; Format is number of terms (int) and for all terms an amplitude (real)
> >> ; and a phase angle (real)
> >> E-x                      =
> >> E-xt                     =
> >> E-y                      =
> >> E-yt                     =
> >> E-z                      =
> >> E-zt                     =
> >>
> >> ; User defined thingies
> >> user1-grps               =
> >> user2-grps               =
> >> userint1                 = 0
> >> userint2                 = 0
> >> userint3                 = 0
> >> userint4                 = 0
> >> userreal1                = 0
> >> userreal2                = 0
> >> userreal3                = 0
> >> userreal4                = 0
> >>
> >>
> >> In the log file it is written that RMS force on the shell is -nan and
> it
> >> can't do EM.
> >> Can someone give me some advice in order to make EM possible?
> >>
> >
> > Please provide full details about what the system is and how you built
> > it.  Also note that using plain cutoff electrostatics went out of style
> > about 20 years ago as it is horribly inaccurate.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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